Through the Darkness Genesis
by Spartan-259 Raphael
Summary: Admiral Raphael and his Brother Jason have to find out their true heritage and fight a new enemy that can destroy their entire universe. To save their universe, they must journey to others and gather allies for the coming war.
1. Chapter 1

**I do not own Halo at any time. Trust me. Now this is a story I've been working on for 3 months. So I would appreciate it if you only criticized me and didn't flame me. Now I had a partner in this with me called InvizibleDragon. We have been working on this for a very long time, Now onto what's going to make this story.**

**Summary: Admiral Raphael and his Brother Jason to find out their true heritage and find a new enemy that can destroy their entire universe. To save their universe, they must journey to others and gather allies.**

**Pairings: Oc x Oc x Harem: This means that Raphael and Jason Share the harem. If you want to see their Bios look on my Profile page and look them up. It'll explain everything.**

**Naruto x Harem: While my characters are in the story I hate leaving Naruto out to fend for himself. You'll see the Harem list on my Profile Page.**

**Now I really hope you enjoy my story and enjoy reading it. Onto the Story:**

**(Aboard the "Through the Darkness")**

I walked through the halls of the ship, the new Spartan-Class vessel. Only three were ever made, after the war the UNSC wanted to create a vessel that rivaled any and all foes. And thus, the Spartan class was born. It was a very large vessel, approximately the same length as a Covenant Super Carrier. It was the most technologically advanced vessel of the UNSC. It was equipped with a Super MAC cannon and two smaller Mac cannons. It was also equipped with a Point Defense Grids. And it can also house two frigates for repair or restock. The Spartan classes were meant to be a Flying Fortress .

After the war, it was relatively peaceful, though the Sangheili relations were strained, we were at peace and were in reconstruction phase, Building up population, rebuilding and terraforming planets. Reach was the first to be Terraformed, we recovered many bodies, Soldiers, Civilians, Children… Spartans. Spartans…my brothers and sisters. That's right… I'm a Spartan, a Two to be exact, I trained and fought with John, my brother was as well. Jason was wart of the Odens eye Project. I sighed and remembered how my brother acted even after he escaped and we met at New Mombasa. He was a very laid back and always joked, but when he was in battle… he was a Gaurdian Angel, he saved me countless times, from either Brutes or anything I couldn't handle with my Sniper Rifle alone. He was my brother in all but blood.

I stood looking over the planet, Earth. It was a beautiful planet. I was a part of the homefleet. It was a boring job, but one that must be done. I was born on Harvest, a cold planet, but I was happy with my mother Athena, she was a very beautiful woman. She often told me I wasn't her son but I loved her much like a son would. When I hit six, she told me that men would take me away from her and she said not to be scared, Often reassuring me. I didn't understand, other of my brothers weren't informed that they were being taken, why was mine? I shrugged it off and it could've been a leak in information. I sighed and looked out to endless vastness of space. It was beautiful, but even beauty has dark secrets. The war with the covenant has shown us that.

Jason strolled over with a beer in hand, strange; I didn't know UNSC allowed drinking on the job. Then again he was off duty so I just shrugged it off and continued looking out.

"Still thinking huh?" Jason asked taking another sip from his beer. It was a red can, so I assumed it was Tecate, the Mexican beer. I laughed and sat back down in my seat and sighed happily.

"nah, just thinking of the old days with John and Johnson… I miss them both" I sigh sadly and looked at the floor, remembering a good friend, and a brother. He stopped drinking for a minute, remembering the days from the war.

"It was hell, we lost most if not all of our family and nearly lost the war." He said putting his beer can down onto the stand and sighed, we were there when we went after Cortana on High Charity, we were there when Johnson was killed by 343 Guilty Spark. We were there when Reach fell and glassed. We were there at each and every one of these, hoping to make some difference in each battle. Reach… oh hell… Reach was and still is my biggest regret, its one thing I felt I could have done more for. Many argue that I did all I could but… to me it doesn't feel that way. But I moved on, even if I still have nightmares to this day.

I then heard a call come over on comm.

"On screen" I told a crew member who nodded and put the comm on screen, On screen came on Fleet Admiral Lord Hood. We have been under his command since I received the second Spartan-Class to be built. We were friends with the Admiral, often helping when the other needed. I saluted and looked towards the fleet admiral.

"Lord Hood" he nodded and I sat back in the seat. He looked at me then began to speak.

"Good morning Admiral Raphael, I trust everything is going well?" he asked looking at me then to my brother Jason.

"So far so good, Jiralhanae forces and Shan'Shayum forces haven't been heard from in a few months. Thank god" I said looking over a few reports that some of the crew gave me to look over. He sighed and looked over a file and finally looked at me once again.

"Good, but we have a mission for you, it's important, head to Sangheilos, meet with Thel. He says that he may have a way to improve relations with humans. It's a plan so we don't know how it will work" I smiled lightly, remembering Thel, besides John, I was a very close friend of his and we looked forward to fighting alongside one another again. I even saved him once or twice, even if he won't admit it, his pride wont let him do so.

"Understood, do we know what this plan is or are we going in blind?" I asked looking at the very powerful man in the military. I coughed a little, for a while I have been getting sick with a cough but I kept it low, no need to show the guys in armor that I need protecting.

"You are going in blind, we have three options, you can take one, two or hell all three. He will inform you when you get there" I nodded and saluted before the comms was cut off and I sat back in my seat. Jason chuckled at me taking another sip if his beer.

"What do you think it is?" he asked me looking at me while leaning against the commander's chair. I sighed and ran my hand through my silver hair. I sighed and chuckled.

"Now whats the fun in telling, guessing is all the fun! I want all hands prepared for a Slipspace Jump, I want to be at Sangheilios ASAP" I said with a smile, getting to see an old friend after such a long time.

"Whats got you so Happy?" he asked with a smirk, crushing the can with his strength and chucking it in the trash can, with perfect accuracy. I chuckled and leaned back.

"Just glad to see an old friend again, I know you don't trust aliens, soooo you'll be staying onboard, this allows me to catch up with an old friend and see whats up" he nods and pulls out a water bottle.

"Entering Slipspace in five…" said navigation and I braced against the chair as we entered the portal and blackness of slipspace.

(3 hours later)

"ETA Motoko?" I asked the Onboard AI, she was based off Motoko Kusanagi from the hit show Ghost in the Shell. I chuckled as Motoko appeared ticked at me.

"Another day and a half, why are you so worried? I swear your more worried than Jason when you saved his ass from a Fuel Rod Cannon Round" she said making a holographic book appear out of thin air and began reading it.

"Hey in my defense I hate to see this idiot hurt" said Jason walking up to the bridge, munching on a piece of Bacon. He loved meat, and ate it almost every day. I rolled my eyes at him and shook my head.

"Moving on!" I said trying to steer away from the conversation. I stood and stretched, popping joints. "Ugh, I need to hit the gym soon" I stood and smirked at Jason. "Yet who saved your ass on New Arcadia?" I said with a chuckle.

"Hey that brute was quiet, I was too focused on the wraiths" I shook my head and pulled a knife and a wooden block from a small chest next to my c hair and began carving. I loved creating things, making peoples thoughts into reality. Carving or Drawing helped me learn that, I guess creating was one thing I enjoyed.

Halfway through the carving I set it done and looked out the window, seeing the dark vastness of space. But then something caught my eye, I looked closer and it… looked like a ship. I shook my head. "That's not possible" I looked out again and for a second I didn't just see one ship, I saw an entire armada, but just as I saw it, it vanished, as though it were never there. It unnerved me to no end. Was this an Omen? A warning? I sure hope not but just to be safe.

"Motoko, I want a scan as far as you can possibly go" I asked her still looking at the same spot. If this was a sign, im not going to ignore it.

"What are you talking about? Were in Slipspace, no one is out here but us."

"I'm not so sure, just please, check" she nods disappears to do the reading. After a few minutes she came back up on the holopad.

"I detected Something for a second then it vanished, maybe it was a bug in the system" I nodded at her in thanks and sat back in my chair. Something was coming, what I'm not sure… but I hope it isn't a repeat of The Great War….

**AAAAAND that's a Wrap! Wahoooo! I finally did the remake of this story. I will be having a poll on what should be done with the Sangheili and Humans. Like Hood said, there are three options, I will post the poll soon after this chapter is up. If anyone has ideas on what one should be PM me or InvizableDragon. My Co-Writer in all of this. He helped me put this story up so as such he should get as much recognition as I or anyone else. **

**Anyway… we will be doing about twenty crossovers, I will post the list on my Profile when I get the chance but im sure you all will love the line-up. A few other things before I wrap this up. Lots of people have been asking me to update, I will… but im currently in collage and I have butterfingers so Laptops with me don't last long. I hope to break that record and keep this laptop for a looooooooong time. Well if not I can always find a way to write the stories another way.**

**If You have a Crossover you wanna see… PM me, or InvizableDragon, if we seen it and have knowledge of it then we will most Certainly do it, but me and my friend have to first agree. If anyone is a better artist than I am then please PM, while I can draw, I want stuff that looks professional. If nothing else Ja Ne.**


	2. Chapter 2

**I do not own Halo at any time. Trust me. Now this is a story I've been working on for 3 months. So I would appreciate it if you only criticized me and didn't flame me. Now I had a partner in this with me called InvizibleDragon. We have been working on this for a very long time, now onto what's going to make this story.**

**Summary: Admiral Raphael and his Brother Jason to find out their true heritage and find a new enemy that can destroy their entire universe. To save their universe, they must journey to others and gather allies.**

**Pairings: Oc x Oc x Harem: This means that Raphael and Jason Share the harem. If you want to see their Bios look on my Profile page and look them up. It'll explain everything.**

**Naruto x Harem: While my characters are in the story I hate leaving Naruto out to fend for himself. You'll see the Harem list on my Profile Page.**

**Now I really hope you enjoy my story and enjoy reading it. Onto the Story:**

**(Aboard the "Through the Darkness")**

We're arriving to Sangheilos ahead of schedule. Something I'm grateful for, the one thing I'm not is twenty Sangheili ships seemingly glaring at me, as if taunting me to do something. I shook my head and sat in the commander's chair and looked at the alien planet.

"Contact Thel, tell him we're here" Motoko appears atop the hologram pad and nods and begins typing on a keyboard she materialized. I chuckled and sat back watching the twenty or so Sangheili ships moving in perfect sync, in perfect formation. I sat playing with an old quarter, an old fashioned quarter. I sighed and looked at the quarter. '_Am I broken? Just like ONI says, am I less human simply for being a Spartan?_' I asked myself looking at the quarter before flipping it high into the air before catching it.

"Thel is granting you permission to land, don't do anything stupid, I don't want to tell the others why you ended up dead with a sword in the gut" I stood up with an amused smirk and chuckled.

"No promises, set us down, no need to keep them waiting" I said putting the coin in my pocket and put on my admiral uniform. It was similar to lord hoods, but in black, seeing as I'm a Spartan. I put a pistol on my hip and had a knife on my left hip. Personally I don't believe I'll need it but as they say "Better to have it and not need it then need it and not have it." I chuckled and left the ship with no escort. I am a Spartan, not to say I'm arrogant, I can handle myself just fine thank you. I stepped off of the ship to be greeted with the sight of Thel with two guards beside him. I smiled brightly and walked over to my long time friend and shook his hand.

"Thel! My friend its so good to see you again" I shook his hand with a firm grip. He smiled and looks at me.

"Likewise Spartan. Or should I say Fleetmaster?" he chuckled as I rubbed the back of my head nervously. I often hated titles, and always thought that people shouldn't be respected by their titles but their accomplishments.

"well… to you and the rest of my friends its just Raphael" he chuckled and led the way into the great city that stood before me. It was a beauty, after many years, this is the first time I ever stepped foot on Sangheilos. I of course enjoyed being and going to different planets. I chuckled as many Sangheili gave me looks of respect and even one or two of lust. Thel chuckled at what he had planned, I of course gave him a curious look and he looked at me.

"Don't worry my friend, you'll like a few of the choices I have in mind" he led the way into a room guarded by six Honor Guards. He signaled for the two guards following us to stay behind and motioned me into the room. "I hear you're here to help with relations between our people" I nod and sit on a chair across from his desk.

"I am here to help, how about a spar as we talk?" he nods and clears the desk and chairs out of the way, I remove my armor and shirt, leaving me and Thel with nothing but the waist up. I took a boxing position and he took his own position and nodded to him. I took the first swing, he blocked it, deflecting it and punching me in the armpit. I winced. "So what are these proposals?" I asked backing off and taking my boxer position once again. I looked at his stance and analyzed it like any Spartan would, trying to find an opening, None that I saw. I guess I had o just wing I and hope I got a hit.

"The first is allowing my son onto your ship, allowing him to learn from the best." I looked at him curiously, he then threw a left hook and I dodged and clotheslined his stomach, making him back off a few before recovering and he threw a kick which hit me dead in the chest. I fell back and stood once more looking at my old friend.

"Son? I'm sure can, what is he? A minor?" I asked waiting for him to make the next move, I blocked a punch to the midsection and countered it with a quick jab to the stomach. He backed off and went into a defensive stance. Thel chuckled and shook his head. and threw a punch which I prepared for, in the middle of delivering the punch he spoke.

"No, he's a Special Operations." I did a double take, which allowed Thel to give him the chance to hit me hard in the chest, I oof'ed and hit the ground hard. He chuckled and pulled me up, and I rubbed my chest where Thel had hit me. He had a smile on his face, I shook my head and popped my back.

"You have Great timing Thel" he chuckled and I dusted myself off. I went back into a fighting stance and and began to throw a second punch to the chest."I thought it was humorous" he said with a smile on his face, I shook my head and looked at the Sangheili.

"I didn't, but besides that, he's Special Operations already? Whats the point in me training him then?" I looked at the Sangheili, thinking of hundreds of methods. Thel shakes his head and reworded my earlier statement.

"No, you see… he was born and raised on a human world, try and mend relations, so he may act-" I interrupted him there. I knew where he was going with this. I knew Jason probably wouldn't like it but, who knows… I might like him.

"Different?" I said with a smirk. He shook his head and put his armor back on, I did the same and pitting my pistol and knife back on my thigh. i chuckled at the thought of a Sangheili acting like a teenage human., enjoying music and checking out women, both human and Sangheili.

"Think you can handle a teenage Special Operations Officer?" he asked with a smile and sitting back down in his seat. I laughed and remembered something.

"Hey I handle Jason and Jamey aboard my ship, sure, now what are the others?" I asked Thel as I took the folder and placed it in a bag I carried.

"The next, is integrate a Sangheili ship into your fleet." I looked at him curiously at this, and then shook my head. Some marines may enjoy having Sangheili around, most wont though. Its been five years since the war.

"Hood, I swear I will haunt you when I die, I can do that one, just as long as they dont kill me, I've always been the sneaky type, it comes with the territory of being a sniper" I said knowing the Sangheili sense of Honor. He nods and hands me the file which I put it in the pack.

"Now as amusing as haunting the fleetmaster is I will give you the last file to read on your own" he passed over the file which I looked at Thel curiously. I grabbed the file and began reading it over and halfway through I widened my eyes.

"I have to WHAT?!" Thel seemed to have a smirk on his face that his long time friend has lost his composure over a simple request.

"And here I thought you were calm and collected most of the time my friend" he said fixing up his desk of the clutter.

"Yeah well in my defense I'm proposed with marriage to a in human terms a princess." I told my friend before continuing to look over the contract. I sighed and stood and put the file in my pack and projected my arm forward to shake Thel's hand. He took it and I smiled.

"Looks like I'm getting tied down… Jamey wont like it though" I chuckled and tried to push the on coming doom to the back of my mind. He grabbed my hand and gave it a firm shake. I smiled and we sat around talking and catching up as old friends.

(Back on the Darkness)

"So how'd it go?" Asked my long time brother and friend Jason, I shook my head in amusement and sat in the commanders chair. I chuckled and handed him the first two files. He looked them over and shook his head, then I handed him the last one. He read this one over and busted out laughing.

"Oh man, Jamey is goonna love this! Hmmm… should I call you prince now?!" he continued laughing in sheer amusement at the prospect before leaning on the wall for support. I smacked the guys shou;der and took back the datapad.

"We should be seeing Thel's son aboard soon." Jason shook his head and headed back to his bunk, I just sat there looking at the datapads sighing. I am so going to get Thel back for this. Somehow, I have no clue as to what to do when he gets aboard… I hate the uknown, but we make use of what we can I guess. I sighed and put the datapad in my pack and leaned back into my seat, soon, I can head home and relax… just Hood decided not now… I'm going to haunt him when I die. I chuckled at the thought…

**I AM DONE! YES! Ok so I know I promised this one once a week but I have been busy before I signed up for school and wanted to get this out before… I well… went to school. I for one love this story and been wanting to get this story out and soooon. I have so much work to do on my stories its not even funny. But on brighter news I am doing lots of crossovers with Halo, so if you want to see a specific crossover, PM me or Invizable Dragon and we will get back to you on that idea.**

**A few more things, unfortunately I start school… soon… soooooo I wont have as often to update my stories as I want to…. I appolagize in advance but I Promise that I will post as many as I can when I can… please just send me as many reviews as possible. Tell me, good? Bad? NO FLAMERS! I HATE THEM! THEY DESTROY PEOPLES HARD WORK WHEN THEY DON'T HAVE THE GALL TO TRY THE IDEA AND SHOW THEM HOW ITS DONE! SO FLAMERS NOW… SHUT UP! That's is all… but other than that, I got a new PSP so that will also cut into my time and wont be able to update as I want.**


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